Question: Gene annotation pipeline for bacteria
gravatar for bird77
22 months ago by
bird7720 wrote:

I have a draft genome of a alpha-proteobacterium (genome size about 8Mbp) and I want to perform gene prediction and annotation.

Until now, I have used the RAST server for this task, but the amount of predicted genes with the annotation "hypothetical protein" is very high (about 60%).

What can you recommend for prokaryotic gene prediction and annotation workflows (I certainly can also combine different tools for gene prediction and annotation, but I do not know what the current standard is)?

Thank you so much for your assistance.

annotation genome • 932 views
ADD COMMENTlink modified 10 months ago by predeus690 • written 22 months ago by bird7720
gravatar for colindaven
22 months ago by
Hannover Medical School
colindaven840 wrote:

Have a look at Prokka by Torsten Seeman, or the recent Genix.

Other places also have web based annotation pipelines, the NCBI one probably still exists.

ADD COMMENTlink written 22 months ago by colindaven840
gravatar for predeus
10 months ago by
predeus690 wrote:

Prokka is probably most used in the field now. Using --proteins with a specific database (e.g. species-specific) seems like a good way to annotate most of the ORFs. Just make sure you get the reference proteins in the right format - they need to look something like this:

>gene_id ~~~gene_name~~~putative protein function

There are few scripts to make your protein annotations look like this. the problem is discussed in one of the issues on Prokka github repository.

ADD COMMENTlink written 10 months ago by predeus690
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